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PDBsum entry 1ds5

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protein ligands metals Protein-protein interface(s) links
Transferase PDB id
1ds5
Jmol
Contents
Protein chains
328 a.a. *
16 a.a. *
18 a.a. *
Ligands
AMP ×4
Metals
_MG ×4
Waters ×337
* Residue conservation analysis
PDB id:
1ds5
Name: Transferase
Title: Dimeric crystal structure of the alpha subunit in complex with two beta peptides mimicking the architecture of the tetrameric protein kinase ck2 holoenzyme.
Structure: Casein kinase, alpha chain. Chain: a, b, c, d. Synonym: ck2. Engineered: yes. Casein kinase, beta chain. Chain: e, f, g, h. Fragment: residues 181-203. Synonym: ck2. Engineered: yes
Source: Zea mays. Organism_taxid: 4577. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Other_details: synthetic peptide corresponding to the sequence 181-203 of the beta-subunit of human protein kinase ck2.
Biol. unit: Tetramer (from PQS)
Resolution:
3.16Å     R-factor:   0.214     R-free:   0.289
Authors: R.Battistutta,S.Sarno,E.De Moliner,O.Marin,G.Zanotti, L.A.Pinna
Key ref:
R.Battistutta et al. (2000). The crystal structure of the complex of Zea mays alpha subunit with a fragment of human beta subunit provides the clue to the architecture of protein kinase CK2 holoenzyme. Eur J Biochem, 267, 5184-5190. PubMed id: 10931203 DOI: 10.1046/j.1432-1327.2000.01587.x
Date:
07-Jan-00     Release date:   07-Jan-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P28523  (CSK2A_MAIZE) -  Casein kinase II subunit alpha
Seq:
Struc:
332 a.a.
328 a.a.
Protein chains
Pfam   ArchSchema ?
P67870  (CSK2B_HUMAN) -  Casein kinase II subunit beta
Seq:
Struc:
215 a.a.
16 a.a.
Protein chain
Pfam   ArchSchema ?
P67870  (CSK2B_HUMAN) -  Casein kinase II subunit beta
Seq:
Struc:
215 a.a.
18 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chains A, D: E.C.2.7.11.1  - Non-specific serine/threonine protein kinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + a protein = ADP + a phosphoprotein
ATP
+ protein
=
ADP
Bound ligand (Het Group name = AMP)
matches with 85.00% similarity
+ phosphoprotein
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     phosphorylation   2 terms 
  Biochemical function     nucleotide binding     7 terms  

 

 
    reference    
 
 
DOI no: 10.1046/j.1432-1327.2000.01587.x Eur J Biochem 267:5184-5190 (2000)
PubMed id: 10931203  
 
 
The crystal structure of the complex of Zea mays alpha subunit with a fragment of human beta subunit provides the clue to the architecture of protein kinase CK2 holoenzyme.
R.Battistutta, S.Sarno, E.De Moliner, O.Marin, O.G.Issinger, G.Zanotti, L.A.Pinna.
 
  ABSTRACT  
 
The crystal structure of a complex between the catalytic alpha subunit of Zea mays CK2 and a 23-mer peptide corresponding the C-terminal sequence 181-203 of the human CK2 regulatory beta subunit has been determined at 3.16-A resolution. The complex, composed of two alpha chains and two peptides, presents a molecular twofold axis, with each peptide interacting with both alpha chains. In the derived model of the holoenzyme, the regulatory subunits are positioned on the opposite side with respect to the opening of the catalytic sites, that remain accessible to substrates and cosubstrates. The beta subunit can influence the catalytic activity both directly and by promoting the formation of the alpha2 dimer, in which each alpha chain interacts with the active site of the other. Furthermore, the two active sites are so close in space that they can simultaneously bind and phosphorylate two phosphoacceptor residues of the same substrate.
 
  Selected figure(s)  
 
Figure 2.
Fig. 2. Space-filling representation of the dimer formed by CK2- subunits (green and blue) with two C-terminal peptides (red and magenta) of CK2- regulatory subunit (A) and corresponding stereo drawing of the same tetramer (B). (A) Interacting monomers are related by a twofold axis, roughly perpendicular to the plane of the paper. (B) Only the C atoms are shown for the two subunits (A6 to A333 and B6 to B333), along with all the atoms of the two peptides (E and F) from residues 188–203. The position of the active sites is illustrated by the two nucleotides, shown as ball-and-stick.
Figure 4.
Fig. 4. Stereo drawing of the CK2 tetramer active sites. Relevant residues from one chain (green) interacting with residues from the second chain (yellow) are shown as ball-and-stick. Arg-A47 points toward the nucleotide bound in the active site of CK2- -B and vice versa. Interactions involving Lys-A44, Arg-A47, Glu-A52, Asp-B120, Lys-B122 and His-B160 of the two chains and His-F193 of a peptide (see text) are emphasized by dashed black lines.
 
  The above figures are reprinted by permission from the Federation of European Biochemical Societies: Eur J Biochem (2000, 267, 5184-5190) copyright 2000.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19925455 M.A.Pagano, O.Marin, G.Cozza, S.Sarno, F.Meggio, K.J.Treharne, A.Mehta, and L.A.Pinna (2010).
Cystic fibrosis transmembrane regulator fragments with the Phe508 deletion exert a dual allosteric control over the master kinase CK2.
  Biochem J, 426, 19-29.  
17097160 B.C.Jensen, C.T.Kifer, D.L.Brekken, A.C.Randall, Q.Wang, B.L.Drees, and M.Parsons (2007).
Characterization of protein kinase CK2 from Trypanosoma brucei.
  Mol Biochem Parasitol, 151, 28-40.  
  15951851 A.C.Bibby, and D.W.Litchfield (2005).
The multiple personalities of the regulatory subunit of protein kinase CK2: CK2 dependent and CK2 independent roles reveal a secret identity for CK2beta.
  Int J Biol Sci, 1, 67-79.  
16335523 K.Niefind, and O.G.Issinger (2005).
Primary and secondary interactions between CK2alpha and CK2beta lead to ring-like structures in the crystals of the CK2 holoenzyme.
  Mol Cell Biochem, 274, 3.  
15108354 E.Grasselli, V.Tomati, M.V.Bernasconi, C.Nicolini, and L.Vergani (2004).
C-terminal region of protein kinase CK2 alpha: How the structure can affect function and stability of the catalytic subunit.
  J Cell Biochem, 92, 270-284.  
15273306 N.Kannan, and A.F.Neuwald (2004).
Evolutionary constraints associated with functional specificity of the CMGC protein kinases MAPK, CDK, GSK, SRPK, DYRK, and CK2alpha.
  Protein Sci, 13, 2059-2077.  
15060571 O.Filhol, J.L.Martiel, and C.Cochet (2004).
Protein kinase CK2: a new view of an old molecular complex.
  EMBO Rep, 5, 351-355.  
12700239 D.H.Song, I.Dominguez, J.Mizuno, M.Kaut, S.C.Mohr, and D.C.Seldin (2003).
CK2 phosphorylation of the armadillo repeat region of beta-catenin potentiates Wnt signaling.
  J Biol Chem, 278, 24018-24025.  
11956194 S.Sarno, P.Ghisellini, and L.A.Pinna (2002).
Unique activation mechanism of protein kinase CK2. The N-terminal segment is essential for constitutive activity of the catalytic subunit but not of the holoenzyme.
  J Biol Chem, 277, 22509-22514.  
11574463 K.Niefind, B.Guerra, I.Ermakowa, and O.G.Issinger (2001).
Crystal structure of human protein kinase CK2: insights into basic properties of the CK2 holoenzyme.
  EMBO J, 20, 5320-5331.
PDB code: 1jwh
11260493 M.Riera, G.Peracchia, E.de Nadal, J.Ariño, and M.Pagès (2001).
Maize protein kinase CK2: regulation and functionality of three beta regulatory subunits.
  Plant J, 25, 365-374.  
11746948 R.L.Rich, and D.G.Myszka (2001).
Survey of the year 2000 commercial optical biosensor literature.
  J Mol Recognit, 14, 273-294.  
11015211 S.Sarno, O.Marin, M.Boschetti, M.A.Pagano, F.Meggio, and L.A.Pinna (2000).
Cooperative modulation of protein kinase CK2 by separate domains of its regulatory beta-subunit.
  Biochemistry, 39, 12324-12329.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.